GapMind for catabolism of small carbon sources

 

Protein WP_040659554.1 in Oscillibacter ruminantium GH1

Annotation: NCBI__GCF_000307265.1:WP_040659554.1

Length: 511 amino acids

Source: GCF_000307265.1 in NCBI

Candidate for 21 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-mannose catabolism HSERO_RS03640 lo Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 38% 97% 334.3 Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- 43% 387.1
D-cellobiose catabolism mglA lo Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 39% 99% 333.6 Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- 43% 387.1
D-glucose catabolism mglA lo Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 39% 99% 333.6 Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- 43% 387.1
lactose catabolism mglA lo Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 39% 99% 333.6 Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- 43% 387.1
D-maltose catabolism mglA lo Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 39% 99% 333.6 Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- 43% 387.1
sucrose catabolism mglA lo Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 39% 99% 333.6 Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- 43% 387.1
trehalose catabolism mglA lo Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 39% 99% 333.6 Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- 43% 387.1
D-xylose catabolism xylG lo Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 39% 99% 333.6 Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- 43% 387.1
myo-inositol catabolism PS417_11890 lo m-Inositol ABC transporter, ATPase component (itaA) (characterized) 38% 94% 328.6 Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- 43% 387.1
D-fructose catabolism frcA lo ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 38% 96% 315.8 Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- 43% 387.1
sucrose catabolism frcA lo ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 38% 96% 315.8 Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- 43% 387.1
L-fucose catabolism BPHYT_RS34245 lo ABC transporter related; Flags: Precursor (characterized, see rationale) 33% 98% 270 Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- 43% 387.1
L-rhamnose catabolism BPHYT_RS34245 lo ABC transporter related; Flags: Precursor (characterized, see rationale) 33% 98% 270 Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- 43% 387.1
L-alanine catabolism braG lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 87% 111.7 Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- 43% 387.1
L-isoleucine catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 87% 111.7 Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- 43% 387.1
L-leucine catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 87% 111.7 Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- 43% 387.1
L-proline catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 87% 111.7 Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- 43% 387.1
L-serine catabolism braG lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 87% 111.7 Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- 43% 387.1
L-threonine catabolism braG lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 87% 111.7 Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- 43% 387.1
L-valine catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 87% 111.7 Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- 43% 387.1
L-proline catabolism HSERO_RS00900 lo ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 30% 91% 107.5 Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- 43% 387.1

Sequence Analysis Tools

View WP_040659554.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MSTEQASTSAGQLLSVQNIRKSFGLNAVLKGISLDVAPGEILALVGGNGAGKSTLMKIIM
GIYTQDGGDIYIKGEHVVLNKPAQALAKGIYMVPQEPLLFPNMTVEENITIGFSQNKAEL
HRELVATMDEIGWHLNLTRRASSLSIAEQQLVEILRGLLRHAQILILDEPTSALTFDEVE
SLFKCVRDLQSKGIGIIYITHRLTEVFELATHVAIMRDGIIAVKGAVSGFTREDLVRGLL
PPDMDACKDGGCPVPTAVDYTKAPVLELQNFGGYGFSGINLKIYPGEILGMAGVVGAGRT
ELATTIFGMDKVLGGKVLLNGRDITGLKTRAVIQAGLNYVPEDRHLNGLFKISDVACNTS
SALLGDGSLGKFLLNRKKEQTLTQRYVDDFRTKITGQEQAVGSLSGGNQQKVVIARSLST
SPRVIILDEPTRGIDAAARGDVYRIIHQLRDQGVSILLISSDMEEIVELADRAVTVFQGR
VNGEFKGADINQDRLMAAAFGVSEEKVASGS

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory